I've recently bought an SSD and replaced my laptop's DVD drive space with the stock HDD, so that I cound install the SSD on the HDD port. However, I've noticed that the HDD is now sometimes going into "Standby" or "sleep" mode (when I'm not using the HDD), where it stops (probably in order to save power). This type of behaviour seems to be specific to the secondary SATA port alone, so I'm wondering if it's just something designed only for DVD drives, and whether is it healthy for the HDD to suffer from such speed ups and slowdowns?
This behaviour is normal for all SATA drives. After a configurable period of idleness the drive is allowed to initiate a move to standby mode.
This is an option which can be disabled (e.g. with Hdparm -S0), or set to any period between 5 seconds and 20 minutes.
I am guessing that this came preset on your HDD, but that the OS accessed the drive (e.g. for writing logfiles) before the timer triggered. Thus preventing it from entering standby mode.
When you moved the OS to another drive (the SSD) these accesses no longer occur to the HDD, and it finally spins down.
As for the healthy or not: It depends.
There is wear and tear while the disk is spinning. Powering it down reduces that.
There is a lot more wear and tear on the drive during spin-up.
So if you spin down and up every 5 minutes then this is a very bad thing. If the drive spins down and is not used for several days then it might be an advantage.
So much for wear and tear. There is a second aspect: power usage. (Especially on a laptop). Which means the best settings boil down to your usage pattern and your desires.